Phylogeny and classification of the Digenea (Platyhelminthes : Trematoda)

Complete small subunit ribosomal RNA gene (ssrDNA) and partial (D1-D3) large subunit ribosomal RNA gene (lsrDNA) sequences were used to estimate the phylogeny of the Digenea via maximum parsimony and Bayesian inference. Here we contribute 80 new ssrDNA and 124 new lsrDNA sequences. Fully complementary data sets of the two genes were assembled from newly generated and previously published sequences and comprised 163 digenean taxa representing 77 nominal families and seven aspidogastrean outgroup taxa representing three families. Analyses were conducted on the genes independently as well as combined and separate analyses including only the higher plagiorchiidan taxa were performed using a reduced-taxon alignment including additional characters that could not be otherwise unambiguously aligned. The combined data analyses yielded the most strongly supported results and differences between the two methods of analysis were primarily in their degree of resolution. The Bayesian analysis including all taxa and characters, and incorporating a model of nucleotide substitution (general-time-reversible with among-site rate heterogeneity), was considered the best estimate of the phylogeny and was used to evaluate their classification and evolution. In broad terms, the Digenea forms a dichotomy that is split between a lineage leading to the Brachylaimoidea, Diplostomoidea and Schistosomatoidea (collectively the Diplostomida nomen novum (nom. nov.)) and the remainder of the Digenea (the Plagiorchiida), in which the Bivesiculata nom. nov. and Transversotremata nom. nov. form the two most basal lineages, followed by the Hemiurata. The remainder of the Plagiorchiida forms a large number of independent lineages leading to the crown clade Xiphidiata nom. nov. that comprises the Allocreadioidea, Gorgoderoidea, Microphalloidea and Plagiorchioidea, which are united by the presence of a penetrating stylet in their cercariae. Although a majority of families and to a lesser degree, superfamilies are supported as currently defined, the traditional divisions of the Echinostomida, Plagiorchiida and Strigeida were found to comprise non-natural assemblages. Therefore, the membership of established higher taxa are emended, new taxa erected and a revised, phylogenetically based classification proposed and discussed in light of ontogeny, morphology and taxonomic history. (C) 2003 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All rights reserved.

Standardization of dot-ELISA for the serological diagnosis of toxocariasis and comparision of the assay with ELISA

The dot-enzyme-linked immunosorbent assay (dot-ELISA) was standardized using somatic (S) and excretory-secretory (ES) antigens of Toxocara-canis for the detection of specific antibodies in 22 serum samples from children aged 1 to 15 years, with clinical signs of toxocariasis. Fourteen serum samples from apparently normal individuals and 28 sera from patients with other pathologies were used as controls. All samples were used before and after absorption with Ascaris suum extract. When the results were evaluated in comparison with ELISA, the two tests were found to have similar sensitivity, but dot-ELISA was found to be more specific in the presence of the two antigens studied. Dot-ELISA proved to be effective for the diagnosis of human toxocariasis, presenting advantages in terms of yield, stability, time and ease of execution and low cost.

The insular shelves of the Faial-Pico Ridge (Azores archipelago): a morphological record of its evolution

Shelves surrounding reefless volcanic ocean islands are formed by surf erosion of their slopes during changing sea levels. Posterosional lava flows, if abundant, can cross the coastal cliffs and fill partially or completely the accommodation space left by erosion. In this study, multibeam bathymetry, high-resolution seismic reflection profiles, and sediment samples are used to characterize the morphology of the insular shelves adjacent to Pico Island. The data show offshore fresh lava flow morphologies, as well as an irregular basement beneath shelf sedimentary bodies and reduced shelf width adjacent to older volcanic edifices in Pico. These observations suggest that these shelves have been significantly filled by volcanic progradation and can thus be classified as rejuvenated. Despite the general volcanic infilling of the shelves around Pico, most of their edges are below the depth of the Last Glacial Maximum, revealing that at least parts of the island have subsided after the shelves formed by surf erosion. Prograding lava deltas reached the shelf edge in some areas triggering small slope failures, locally decreasing the shelf width and depth of their edges. These areas can represent a significant risk for the local population; hence, their identification can be useful for hazard assessment and contribute to wiser land use planning. Shelf and subaerial geomorphology, magnetic anomalies and crustal structure data of the two islands were also interpreted to reconstruct the long-term combined onshore and offshore evolution of the Faial-Pico ridge. The subaerial emergence of this ridge is apparently older than previously thought, i.e., before approximate to 850 ka.

Stochastic modelling of the reservoir lithological and petrophysical attributes. A case study of the Middle East carbonate reservoir

Dissertação para obtenção do Grau de Mestre em Engenharia Geológica (Georrecursos)

Molluscicidal and Mosquitocidal Activities of the Essential oils of Thymus capitatus Hoff. et Link. and Marrubium vulgare L.

Steam distillation of essential oils of aerial parts of Thymus capitatus and Marrubium vulgare L. collected at North cost of Egypt yielded 0.5% and 0.2%, respectively. Results of Gas chromatography-mass spectrometry analyses of the two samples identified 96.27% and 90.19% of the total oil composition for T. capitatus and M. vulgare, respectively. The two oil samples appeared dominated by the oxygenated constituents (88.22% for T. capitatus and 57.50% for M. vulgare), composed of phenols, mainly carvacrol (32.98%) and thymol (32.82%) in essential oil of T. capitatus, and thymol (34.55%) in essential oil of M. vulgare. It was evaluated the molluscicidal activity of T. capitatus and M. vulgare essential oils on adult and eggs of Biomphalaria alexandrina as well as their mosquitocidal activity on Culex pipiens. The LC50 and LC90 of T. capitatus essential oil against adult snails was 200 and 400 ppm/3hrs, respectively, while for M. vulgare it was 50 and 100 ppm/3hrs, respectively. Moreover, M. vulgare showed LC100 ovicidal activity at 200 ppm/24 hrs while T. capitatus oil showed no ovicidal activity. It was verified mosquitocidal activity, with LC50 and LC90 of 100 and 200 ppm/12hrs respectively for larvae, and 200 and 400 ppm/12hrs respectively for pupae of C. pipiens.

Establishment of environmental and biological bases to optimise the production of the European clam Ruditapes decussatus (Linnaeus, 1758)

Dissertação para obtenção do Grau de Doutor em Ambiente

A "Portrait" of Book XII of the Æneid: the Mosaic of the «House of the Medusa» (Alter do Chão, Portugal)

This paper addresses the study of a mosaic discovered in 2007 at the archaeological site of Alter do Chão, Portugal, whose central panel represents the penultimate scene narrated in the last Book of the Æneid – a Roman epic composed by the poet Publius Vergilius Maro (70 BC – AD 19), at the request of Gaius Julius Cæsar Octavianus Augustus (63 BC – AD 14): it shows the very moment when Turnus, the Latin king of the Rutuli, kneels before Æneas, considered the precursor to the foundation of Rome (Virgil, Æneid, XII, 926-950).

Analysis of the interaction of polycyclic aromatic compounds in a model organism: integration of genotoxic and histopathological effects

Due to their toxicity, especially their carcinogenic potential, polycyclic aromatic hydrocarbons (PAHs) became priority pollutants in biomonitoring programmes and environmental policy, such as the European Water Framework Directive. The model substances tested in this study, namely benzo[b]fluoranthene (B[b]F), considered potentially carcinogenic to humans and an effector carcinogenic PAH to wildlife, and phenanthrene (Phe), deemed a non-carcinogenic PAH, are common PAHs in coastal waters, owning distinct properties reflected in different, albeit overlapping, mechanisms of toxicity. Still, as for similar PAHs, their interaction effects remain largely unknown. In order to study the genotoxic effects of caused by the interaction of carcinogenic and non-carcinogenic PAHs, and their relation to histopathological alterations, juvenile sea basses, Dicentrarchus labrax, a highly ecologically- and economically-relevant marine fish, were injected with different doses (5 and 10 μg.g-1 fish ww) of the two PAHs, isolated or in mixture, and incubated for 48 h. Individuals injected with B[b]F and the PAH mixture exhibited higher clastogenic/aneugenic effects and DNA strand breakage in blood cells, determined through the erythrocytic nuclear abnormalities (ENA) and Comet assays, respectively. Also, hepatic histopathological alterations were found in all animals, especially those injected with B[b]F and the PAH mixture, relating especially to inflammation. Still, Phe also exhibited genotoxic effects in sea bass, especially in higher doses, revealing a very significant acute effect that was accordant with the Microtox test performed undergone in parallel. Overall, sea bass was sensitive to B[b]F (a higher molecular weight PAH), likely due to efficient bioactivation of the pollutant (yielding genotoxic metabolites and reactive oxygen species), when compared to Phe, the latter revealing a more significant acute effect. The results indicate no significant additive effect between the substances, under the current experimental conditions. The present study highlights the importance of understanding PAH interactions in aquatic organisms, since they are usually present in the aquatic environment in complex mixtures.

Analysis of output properties of the Peroxiredoxin/Thioredoxin/Thioredoxin reductase system

Dissertação de mestrado em Bioinformática

Decapod crustaceans used as food by the Yanomami Indians of the Balawa-ú village, State of Amazonas, Brazil

The Yanomami are a group of South American Indians that live in the rainforest along the borderlands of Brazil and Venezuela. They depend on hunting, gardening and wild food for survival; crustaceans are a highly prized food item in their diet. Taxonomical and ethnozoological aspects of the Yanomami Indians of the Balawa-ú village, state of Amazonas, Brazil, related to the crustaceans are described. Information and specimens were obtained from August to December, 2003. Interviews were conducted with residents of the village and focused on questions about species exploited, indigenous names, modes of capture and use of the species. One shrimp species of the family Palaemonidae (Macrobrachium brasiliense) and two crab species of Trichodactylidae (Sylviocarcinus pictus, Valdivia serrata) as well as two of Pseudothelphusidae (Fredius fittkaui, F. platyacanthus) were recorded. The indigenous names applied to these species are: shuhu, for shrimp, oko and peimatherimi for each of the two pseudothelphusid crabs, and hesiki tôtôrema for both trichodactylid crabs.

Measurement of transverse energy-energy correlations in multi-jet events in pp collisions at s√=7 TeV using the ATLAS detector and determination of the strong coupling constant αs(mZ)

High transverse momentum jets produced in pp collisions at a centre of mass energy of 7 TeV are used to measure the transverse energy--energy correlation function and its associated azimuthal asymmetry. The data were recorded with the ATLAS detector at the LHC in the year 2011 and correspond to an integrated luminosity of 158 pb−1. The selection criteria demand the average transverse momentum of the two leading jets in an event to be larger than 250 GeV. The data at detector level are well described by Monte Carlo event generators. They are unfolded to the particle level and compared with theoretical calculations at next-to-leading-order accuracy. The agreement between data and theory is good and provides a precision test of perturbative Quantum Chromodynamics at large momentum transfers. From this comparison, the strong coupling constant given at the Z boson mass is determined to be αs(mZ)=0.1173±0.0010 (exp.) +0.0065−0.0026 (theo.).

Mutations of the Serine Protease CAP1/Prss8 Lead to Reduced Embryonic Viability, Skin Defects, and Decreased ENaC Activity.

CAP1/Prss8 is a membrane-bound serine protease involved in the regulation of several different effectors, such as the epithelial sodium channel ENaC, the protease-activated receptor PAR2, the tight junction proteins, and the profilaggrin polypeptide. Recently, the V170D and the G54-P57 deletion mutations within the CAP1/Prss8 gene, identified in mouse frizzy (fr) and rat hairless (fr(CR)) animals, respectively, have been proposed to be responsible for their skin phenotypes. In the present study, we analyzed those mutations, revealing a change in the protein structure, a modification of the glycosylation state, and an overall reduction in the activation of ENaC of the two mutant proteins. In vivo analyses demonstrated that both fr and fr(CR) mutant animals present analogous reduction of embryonic viability, similar histologic aberrations at the level of the skin, and a significant decrease in the activity of ENaC in the distal colon compared with their control littermates. Hairless rats additionally had dehydration defects in skin and intestine and significant reduction in the body weight. In conclusion, we provided molecular and functional evidence that CAP1/Prss8 mutations are accountable for the defects in fr and fr(CR) animals, and we furthermore demonstrate a decreased function of the CAP1/Prss8 mutant proteins. Therefore, fr and fr(CR) animals are suitable models to investigate the consequences of CAP1/Prss8 action on its target proteins in the whole organism.

Genomic determinants of the efficiency of internal ribosomal entry sites of viral and cellular origin

Summary : Internal ribosome entry sites (IRES) are used by viruses as a strategy to bypass inhibition of cap-dependent translation that commonly results from viral infection. IRES are also used in eukaryotic cells to control mRNA translation under conditions of cellular stress (apoptosis, heat shock) or during the G2 phase of the cell cycle when general protein synthesis is inhibited. Variation in cellular expression levels has been shown to be inherited. Expression is controlled, among others, by transcriptional factors and by the efficiency of cap-mediated translation and ribosome activity. We aimed at identifying genomic determinants of variability in IRES-mediated translation of two representative IRES [Encephalomyocarditis virus (EMCV) and X-linked Inhibitor-of-Apoptosis (XIAP) IRES]. We used bicistronic lentiviral constructions expressing two fluorescent reporter transgenes. Lentiviruses were used to transduce seven different laboratory cell lines and B lymphoblastoid cell lines from the Centre d'Etude du Polymorphisme Humain (CEPH; 15 pedigrees; n=209); representing an in vitro approach to family structure allowing genome scan analyses. The relative expression of the two markers was assessed by FACS. IRES efficiency varies according to cellular background, but also varies, for a same cell type, among individuals. The control of IRES activity presents an inherited component (h2) of 0.47 and 0.36 for EMCV and XIAP IRES, respectively. A genome scan identified a suggestive Quantitative Trait Loci (LOD 2.35) involved in the control of XIAP IRES activity. Résumé : Les sites internes d'entrée des ribosomes (IRES = internal ribosome entry sites) sont utilisés par les virus comme une stratégie afin d'outrepasser l'inhibition de traduction qui résulte communément d'une infection virale. Les IRES sont également utilisés par les cellules eucaryotes pour contrôler la traduction de l'ARN messager dans des conditions de stress cellulaire (apoptose, choc thermique) ou durant la phase G2 du cycle cellulaire, situations durant lesquelles la synthèse générale des protéines est inhibée. La variation des niveaux d'expression cellulaire de transcription est un caractère héréditaire. L'expression des gènes est contrôlée entre autre par les facteurs de transcription et par l'efficacité de la traduction initiée par la coiffe ainsi que par l'activité des ribosomes. Durant cette étude nous avons eu pour but d'identifier les déterminants génomiques responsables de la variabilité de la traduction contrôlée par l'IRES. Ceci a été effectué en étudiant deux IRES représentatifs : l'IRES du virus de l'encéphalomyocardite (EMCV) et l'IRES de l'inhibiteur de l'apoptose XIAP (X-linked Inhibitor-of-Apoptosis). Nous avons utilisés des lentivirus délivrant un transgène bicistronique codant pour deux gènes rapporteurs fluorescents. Ces lentivirus ont été utilisés pour transduire sept différentes lignées cellulaires de laboratoire et des lignées cellulaires lymphoblastoïdes B du Centre d'Etude du Polymorphisme Humain (CEPH; 15 pedigrees; n=209) qui représentent une approche in vitro de la structure familiale et qui permettent des analyses par balayage du génome. L'expression relative des deux marqueurs fluorescents a été analysée par FACS. Nos résultats montrent que l'efficacité des IRES varie en fonction du type de cellules. Il varie aussi, pour le même type de cellules, selon les individus. Le contrôle de l'activité de l'IRES est un caractère héritable (héritabilité h2) de 0.47 et 0.36 pour les IRES de EMCV et XIAP respectivement. Le balayage du génome a permis l'identification d'un locus à effets quantitatifs [QTL Quantitative Trait Loci (LOD 2.35)] impliqué dans le contôle de l'activité de l'IRES de XIAP.

Pseudarthroses aseptiques des os longs [Pseudarthrosis of the long bones].

5 to 10% of all fractures present with a delayed union, whereas 1 to 5% progress to a nonunion, which can be defined as a fracture older than 6 months and lacks any potential to heal without any further intervention. Different fracture and patient related risk factors exist, and the management of a nonunion needs a thorough clinical, radiological and biological workup to classify them in one of the two main categories, the viable nonunions that need essentially more stability, usually by a more rigid fixation, and the non-viable nonunions that need essentially a biological stimulation by decortication and bone grafting. This treatment still remains the first choice with bony healing obtained in 85 to 95% of cases, but it also comes along with certain risks, and some valuable alternatives exist if chosen on the basis of rigid criteria.

Structure and diversity of endoparasitic infracommunities and the trophic level of Pseudoplatystoma corruscans and Schizodon borelli (Osteichthyes) of the high Paraná river

One hundred and ten specimens of Pseudoplatystoma corruscans (Pimelodidae) and 582 specimens of Schizodon borelli (Anostomidae) collected in the high Paraná River were analyzed. On necropsy 74% of P. corruscans were found to be parasitized; proteocephalidean cestodes presented the greatest number. With regard to S. borelli, the percentage of parasitism reached 19.42% and the nematode Cucullanus pinnai was the most abundant. The absence of correlation between the endoparasitic diversity and the standard length of the two host species indicates that each one presents homogeneity in alimentary behaviour during all its life time, permiting the uniform recruitment of the same species of endoparasites during all its ontogenetic development. Independence of diversity values in relation to sex of P. corruscans and S. borelli evidences that the ecological relationships are similar between males and females in these species. Both host's infrapopulations presented a typical overdispersed pattern of distribution with isolationist characteristics.